Have you every executed a query in SQL Server Management Studio, looked at the execution plan, and noticed that it was a different plan than what was generated on the server?
A potential reason for this could be a different option settings. The options represent the SET values of the current session. SET options can affect how the query is execute thus having a different execution plan. You can find these options in two places within SSMS under Tools -> Options -> Query Execution -> SQL Server -> Advanced.